Typically the HSQLDB that JSK uses runs using in-memory mode, not server mode - see "Server modes" at http://hsqldb.org/doc/guide/running-chapt.html. This means that it's not possible to use a tool like SQL Developer, TOAD, Squirrel etc to connect into it. You can manually write a script to startup the DB in server mode, you will need to change the jdbc connection string in server.xml appropriately. Then you should be able to use an external tool to reach the DB using the same jdbc connection string.
If you just need to make a simple few queries then you can try the query tool that comes with HSQLDB. It's very basic, but has the advantage that you don't need to change the DB mode, it can connect to an in-memory DB of a running JSK. To run it, locate the hsqldb.jar within the JSK and run:
java -cp hsqldb.jar org.hsqldb.util.DatabaseManagerSwing